His research seems to indicate that some leaf-cutter ants have "domesticated" a single lineage of fungi for over 30 million years; Chapela is currently studying this symbiosis from evolutionary and agricultural perspectives, as well as looking for ways to manipulate it.
Chapela was co-author (with his graduate student, David Quist) of a controversial 2001 Nature paper about the flow of transgenes into wild Zea mays ssp.
[4] In 2002 and 2003 a research team had two commercial American companies test 153,000 seeds from 870 maize plants in 125 fields in Oaxaca - the same area Chapela and Quist sampled - for transgenic DNA material.
"[4] Chapela objected to an agreement in which the department and faculty of Plant and Microbial Biology at UC Berkeley took money from Novartis in exchange for a degree of publication scrutiny and trade secrecy, taking a strong position on the issue.
[7][8][9][10] Chapela has also spoken out against the deal between UC Berkeley, University of Illinois, Urbana-Champaign, and British Petroleum to research the development of biofuels, which may involve genetically engineering microorganisms and plants.